List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

Filters: Keyword is Evolution, Molecular  [Clear All Filters]
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Evolution, Molecular
D. Botstein and Fink, G. R., Yeast: an experimental organism for 21st Century biology., Genetics, vol. 189, no. 3, pp. 695-704, 2011.
K. Thornton, Bachtrog, D., and Andolfatto, P., X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution., Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
E. Nabieva, Jim, K., Agarwal, A., Chazelle, B., and Singh, M., Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps., Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila., Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
J. - W. Hong, Hendrix, D. A., and Levine, M. S., Shadow enhancers as a source of evolutionary novelty., Science, vol. 321, no. 5894, p. 1314, 2008.
D. Bachtrog and Andolfatto, P., Selection, recombination and demographic history in Drosophila miranda., Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence., Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
D. Gresham, Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., DeSevo, C. G., Botstein, D., and Dunham, M. J., The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast., PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
S. Heinicke, Livstone, M. S., Lu, C., Oughtred, R., Kang, F., Angiuoli, S. V., White, O., Botstein, D., and Dolinski, K., The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists., PLoS One, vol. 2, no. 8, p. e766, 2007.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure., PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
R. S. Dwyer, Ricci, D. P., Colwell, L. J., Silhavy, T. J., and Wingreen, N. S., Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis., Genetics, vol. 195, no. 2, pp. 443-55, 2013.
J. A. Capra and Singh, M., Predicting functionally important residues from sequence conservation., Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., Pervasive natural selection in the Drosophila genome?, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
G. I. Lang, Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., and Desai, M. M., Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations., Nature, vol. 500, no. 7464, pp. 571-4, 2013.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content., Genome Biol, vol. 6, no. 8, p. R67, 2005.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila., Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., Parallel molecular evolution in an herbivore community., Science, vol. 337, no. 6102, pp. 1634-7, 2012.
P. Andolfatto, J Scriber, M., and Charlesworth, B., No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus., Evolution, vol. 57, no. 2, pp. 305-16, 2003.
Y. Zhen and Andolfatto, P., Methods to detect selection on noncoding DNA., Methods Mol Biol, vol. 856, pp. 141-59, 2012.
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., Maximum entropy models for antibody diversity., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
B. K. Jones, Levorse, J., and Tilghman, S. M., A human H19 transgene exhibits impaired paternal-specific imprint acquisition and maintenance in mice., Hum Mol Genet, vol. 11, no. 4, pp. 411-8, 2002.
P. Andolfatto, Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome., Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., Genomic imprinting of a placental lactogen gene in Peromyscus., Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., Genome sequencing reveals complex speciation in the Drosophila simulans clade., Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
G. I. Lang, Botstein, D., and Desai, M. M., Genetic variation and the fate of beneficial mutations in asexual populations., Genetics, vol. 188, no. 3, pp. 647-61, 2011.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO., PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 2009.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship., PLoS One, vol. 7, no. 8, p. e43888, 2012.
D. J. Brooks, Fresco, J. R., Lesk, A. M., and Singh, M., Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code., Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
J. S. Weitz, Benfey, P. N., and Wingreen, N. S., Evolution, interactions, and biological networks., PLoS Biol, vol. 5, no. 1, p. e11, 2007.
A. S. Putnam, J Scriber, M., and Andolfatto, P., Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species., Evolution, vol. 61, no. 4, pp. 912-27, 2007.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., Correlated evolution of nearby residues in Drosophilid proteins., PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
J. Cande, Goltsev, Y., and Levine, M. S., Conservation of enhancer location in divergent insects., Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
Y. Guan, Dunham, M. J., Troyanskaya, O. G., and Caudy, A. A., Comparative gene expression between two yeast species., BMC Genomics, vol. 14, p. 33, 2013.
M. J. Dunham, Badrane, H., Ferea, T., Adams, J., Brown, P. O., Rosenzweig, F., and Botstein, D., Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae., Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16144-9, 2002.
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., The Capsella rubella genome and the genomic consequences of rapid mating system evolution., Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila., PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
M. D. Chikina and Troyanskaya, O. G., Accurate quantification of functional analogy among close homologs., PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility., Nature, vol. 536, no. 7615, pp. 205-9, 2016.
A. B. Wolf and Akey, J. M., Outstanding questions in the study of archaic hominin admixture., PLoS Genet, vol. 14, no. 5, p. e1007349, 2018.